The Find Neighbors command will find neighbors for the specified variable or observation, based on correlation.
To run this module, type MicroArray | Pattern | Find Neighbor.
Input Data Requirements
This function works on -Omic data types.
- Project & Data: The window includes a dropdown box to select the Project and Data object to be filtered.
- Variables: Selections can be made on which variables should be included in the filtering (options include All variables, Selected variables, Visible variables, and Customized variables (select any pre-generated Lists)).
- Observations: Selections can be made on which observations should be included in the filtering (options include All observations, Selected observations, Visible observations, and Customized observations (select any pre-generated Lists).
- Output name: The user can choose to name the output data object.
- Find neighbors for: Define the variable or observation. By default, Array Studio selects the first selected variable or observation from the Data object.
- Variable: Indicate to find the neighbors for a variable.
- Observation: Indicate to find the neighbors for a observation.
- Correlation method: Define the method to calculate correlation between variables (or observations), available options include Pearson, Kendell, and Spearman correlations (see http://en.wikipedia.org/wiki/Correlation).
- Correlation direction: Define the correlation direction of the neighbors: Availabe options are Positive, Negative, and Both. For instance, if the user selects Positive, only neigbors with positive correlation will be shown in the output.
- Fixed neighbor number: Checking this box allows the user to find a fixed number of neighbors.
- With p-value<:Checking this box allows Array Studio to to output neighbors (with the defined correlation direction) with p-value smaller than the set value.
- Output view: specify the type of visualization of identified neighbors. Available options are HeatmapView, ProfileView, or None.
This function will output a new -Omic data object, containing Table Views for the data and metadata for the neighbors, as well as a Heatmap or Profile View, as selected. An example of the resulting "Pattern" folder and HeatmapView generated by this command is shown below.